Set up

Step 0 Import the needed libraries

#!pip install opencv-python
#!pip install keras-metrics
#!pip install spicy
#!pip install --upgrade tensorflow

This is where we tested the 2 step Model.

In Order to run this please follow the following steps:

    ## Run the imports
    ## Run the functions Download Images, then Copy Images.
    ## Create manually on your directory folders, we created them as img_3, imgPrueba, img_b, img_n, img_m
    ## Run creating_folder_test_spit()
    ## Run create_folder_3_parts()
    ## Create_Folder_Malignant()
    ## Create_Folder_B()
    ## Create_Folder_N()
    ## Run the rest of the function and then run Create_Images
    ## The inputs: Create_images(train_generator,'directory', 'train')
    ## also do it for test data. Do this for the directory for img_3, img_b, img_n, img_m
    ## The delete Image is just to delete but dont run it 
    ## Once you have all the images you can run everything in genertor sector in this same steps. This might take a lot of time. 

import pandas as pd
from sklearn.metrics import f1_score
import requests  
import tensorflow as tf
import seaborn as sn
import os, shutil
import numpy as np
import matplotlib.pyplot as plt
import cv2
from keras import backend as K
import tensorflow as tf
from tensorflow.keras.models import Sequential
from tensorflow.keras.layers import Dense, Conv2D, Flatten, Dropout, MaxPooling2D

import pickle

from tensorflow.keras.preprocessing.image import ImageDataGenerator

from tensorflow.keras import models
from tensorflow.keras import layers
from tensorflow.keras import optimizers
from keras.preprocessing import image
import keras_metrics
from collections import Counter
import random
from spicy import ndimage
import imageio
from sklearn.pipeline import Pipeline

WARNING:tensorflow:From C:\Users\dggua\anaconda3\Lib\site-packages\keras\src\losses.py:2976: The name tf.losses.sparse_softmax_cross_entropy is deprecated. Please use tf.compat.v1.losses.sparse_softmax_cross_entropy instead.

C:\Users\dggua\anaconda3\Lib\site-packages\paramiko\transport.py:219: CryptographyDeprecationWarning: Blowfish has been deprecated
  "class": algorithms.Blowfish,

import pandas as pd
import requests  
import seaborn as sn
import os, shutil
import numpy as np
import matplotlib.pyplot as plt
import cv2

import tensorflow as tf
from tensorflow.keras.models import Sequential, Model
from tensorflow.keras.layers import Dense, Conv2D, Flatten, Dropout, MaxPooling2D, BatchNormalization,Concatenate,Input

import pickle

from tensorflow.keras.preprocessing.image import ImageDataGenerator

from tensorflow.keras import models, layers, optimizers
from keras.preprocessing import image
import keras_metrics

from spicy import ndimage
import imageio

from tensorflow.keras.utils import Sequence, to_categorical

from keras.preprocessing.image import load_img, img_to_array

from PIL import Image
from sklearn.model_selection import train_test_split

from tensorflow.keras.optimizers import RMSprop

Step 1 Organize the images in their respective folders

df = pd.read_csv("fitzpatrick17k.csv")
data = df[df['url'].notna()]
data['label'].value_counts()

####################
three_part = data['three_partition_label'].unique()
d = data.loc[data['three_partition_label']=='benign']
print(three_part)
print(d['label'].unique())

['non-neoplastic' 'benign' 'malignant']
['dermatofibroma' 'syringoma' 'prurigo nodularis' 'nevocytic nevus'
 'porokeratosis of mibelli' 'milia' 'granuloma pyogenic' 'epidermal nevus'
 'naevus comedonicus' 'pilar cyst' 'congenital nevus' 'lymphangioma'
 'pilomatricoma' 'disseminated actinic porokeratosis' 'halo nevus'
 'fordyce spots' 'telangiectases' 'becker nevus' 'pyogenic granuloma'
 'port wine stain' 'nevus sebaceous of jadassohn' 'porokeratosis actinic'
 'seborrheic keratosis' 'mucous cyst']

def download_images():
    for i in range(0 ,len(data)):
        url = data['url'].iloc[i]
    label = data['label'].iloc[i]
    print(i)
    if url == '0':
        print('nan image')
    else:
        headers = {
            'User-Agent': 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10.12; rv:55.0) Gecko/20100101 Firefox/55.0',
        }
        data_url = requests.get(url, headers=headers).content 
        m = 'C:/Users/dggua/Documents/DeepLearning/img/img'+str(i)+'.jpg'
        m = 'C:/Users/liita/OneDrive/Documentos/Nova IMS/Deep learning/Proyecto/Prueba/'+str(label)+'/img'+str(i)+'.jpg'
        f = open(m,'bw') 
        f.write(data_url) 
        f.close() 

def copy_images(source_folder, destination_folder):
    # Get a list of files in the source folder
    files = os.listdir(source_folder)
    # Iterate over files and copy images
    for file in files:
        # Check if the file is an image (you can customize this check based on your requirements)
        if file.endswith('.jpg'):
            source_path = os.path.join(source_folder, file)
            destination_path = os.path.join(destination_folder, file)
            shutil.copy(source_path, destination_path)
            print(f"Copied '{file}' to '{destination_folder}'")

#We create a folder where we are going to get the images, and they are classified by ['non-neoplastic' 'benign' 'malignant']
def create_folder_3_parts():
    # Example usage
    parts = ['train','test','validation']
    for name in parts:
        m = 'C:/Users/dggua/Documents/DeepLearning/img_3/'+name
        os.mkdir(m)
        for i in three_part:
            d = data.loc[data['three_partition_label']==i]
            labels_unique = d['label'].unique()
            mm = m + '/'+ i
            os.mkdir(mm)
            for l in labels_unique:
                l= l.replace(" ", "_")
                source_folder = 'C:/Users/dggua/Documents/DeepLearning/img/'+ name + '/'+l
                destination_folder = mm
                copy_images(source_folder, destination_folder)
create_folder_3_parts()

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#Create a folder for malignant seperation
def Create_Folder_Malignant():
    parts = ['train','test','validation']
    for name in parts:
        m = 'C:/Users/dggua/Documents/DeepLearning/img_m/'+name
        os.mkdir(m)
        d = data.loc[data['three_partition_label']=='malignant']
        labels_unique = d['label'].unique()

        for l in labels_unique:
            l= l.replace(" ", "_")
            mm = m + '/'+ l
            os.mkdir(mm)
            source_folder = 'C:/Users/dggua/Documents/DeepLearning/img/'+ name + '/'+l
            destination_folder = mm
            copy_images(source_folder, destination_folder)
Create_Folder_Malignant()

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#Create a folder for 'benign' seperation
def Create_Folder_B():
    parts = ['train','test','validation']
    for name in parts:
        m = 'C:/Users/dggua/Documents/DeepLearning/img_b/'+name
        os.mkdir(m)
        d = data.loc[data['three_partition_label']=='benign']
        labels_unique = d['label'].unique()

        for l in labels_unique:
            l= l.replace(" ", "_")
            mm = m + '/'+ l
            os.mkdir(mm)
            source_folder = 'C:/Users/dggua/Documents/DeepLearning/img/'+ name + '/'+l
            destination_folder = mm
            copy_images(source_folder, destination_folder)
            
 #Create a folder for non-neoplastic' seperation
def Create_Folder_N():
    parts = ['train','test','validation']
    for name in parts:
        m = 'C:/Users/dggua/Documents/DeepLearning/img_N/'+name
        os.mkdir(m)
        d = data.loc[data['three_partition_label']=='non-neoplastic']
        labels_unique = d['label'].unique()

        for l in labels_unique:
            l= l.replace(" ", "_")
            mm = m + '/'+ l
            os.mkdir(mm)
            source_folder = 'C:/Users/dggua/Documents/DeepLearning/img/'+ name + '/'+l
            destination_folder = mm
            copy_images(source_folder, destination_folder)
                       
Create_Folder_B()
Create_Folder_N()

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def Check_Number_SubFolders():
    print(len(df.label.unique()))
    print(df.three_partition_label.unique())
    print('------')
    for i in df.three_partition_label.unique():
        print(i)
        print(len(df.loc[df['three_partition_label']==i].label.unique()))
        print(len(df.loc[df['three_partition_label']==i]))
        print('....')
    print('------')

data['three_partition_label'].value_counts()

three_partition_label
non-neoplastic    12045
malignant          2260
benign             2231
Name: count, dtype: int64

Split the dataset

def creating_folder_test_spit():
    #This is the directory where the images are stored 
    dw_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/imgPrueba'

    #This is the directory where the images will be stored after the split
    original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img'
    #This is the directory where the images are stored 
    dw_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/imgPrueba'

    #This is the directory where the images will be stored after the split
    original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_3'
    #This is the directory where the images are stored 
    dw_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/imgPrueba'

    #This is the directory where the images will be stored after the split
    original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_n'
    #Directories for the training, validation and test splits
    train_dir = os.path.join(original_dataset_dir, 'train')
     os.mkdir(train_dir)
    validation_dit = os.path.join(original_dataset_dir, 'validation')
     os.mkdir(validation_dit)
    test_dir = os.path.join(original_dataset_dir, 'test')
     os.mkdir(test_dir)

     #Create directories for each label in the training, validation and test splits
     for label in labels:
            train_label_dir = os.path.join(train_dir, label)
            os.mkdir(train_label_dir)
            validation_label_dir = os.path.join(validation_dit, label)
            os.mkdir(validation_label_dir)
            test_label_dir = os.path.join(test_dir, label)
            os.mkdir(test_label_dir)
            
        #Copy the images to the training, validation and test splits keeping the 60-20-20 ratio for each label with at least 53 images and a maximum of 653 images per

    for label in labels:
        label_dir = os.path.join(dw_dataset_dir, label)
        fnames = [f for f in os.listdir(label_dir) if f.endswith('.jpg')]
        np.random.shuffle(fnames)
        n = len(fnames)
        train_size = int(0.6*n)
        validation_size = int(0.2*n)
        test_size = n - train_size - validation_size
        train_fnames = fnames[:train_size]
        validation_fnames = fnames[train_size:train_size+validation_size]
        test_fnames = fnames[train_size+validation_size:]

        for fname in train_fnames:
            src = os.path.join(label_dir, fname)
            dst = os.path.join(os.path.join(train_dir, label), fname)
            shutil.copyfile(src, dst)

        for fname in validation_fnames:
            src = os.path.join(label_dir, fname)
            dst = os.path.join(os.path.join(validation_dit, label), fname)
            shutil.copyfile(src, dst)

        for fname in test_fnames:
            src = os.path.join(label_dir, fname)
            dst = os.path.join(os.path.join(test_dir, label), fname)
            shutil.copyfile(src, dst)

Step 2 Data preprocessing

• Read the picture files.
• Decode the JPEG content to RGB grids of pixels.
• Convert these into floating-point tensors.
• Rescale the pixel values (between 0 and 255) to the [0, 1] interval (as you know, neural networks prefer to deal with small input values).

Read the picture files and load each image file into an array. In which each element corresponds to a pixel with 3 channels with an integer from 0 to 255

Augment

def histogram_eq(img, bines,t):

    #count the number of pixels
    
    img = img
    
    img = img.astype(np.uint8)
    n = img.size
    print(n)
    #Get tje gary level histogram
    r = img.flatten() #0=black 255=white
    hist, bins = np.histogram(r, bines, [0,bines])
    Pf = hist/n

    #Get the cumulative distribution function
    cdf = np.cumsum(Pf)
    T = (bines-1)*cdf
    Trounding = np.round(T).astype('uint8')

    #Apply the transformation
    img_eq = Trounding[r].reshape(img.shape)

    return img_eq

def thresholding(f, L):
    f_tr = np.zeros(f.shape).astype('uint8')  # Initialize to zeros (background)
    f_tr[f <= L] = 255  
    return f_tr

#Otsu thresholding
def otsu_threshold(img):
    max_L = 256
    hist_t, bin_edges = np.histogram(img, bins=max_L, range=(0, max_L))
    M = np.product(img.shape)
    best_threshold = 0
    min_var = float('inf')

    for L in range(1, max_L - 1):
        w_a = np.sum(hist_t[:L]) / M
        w_b = np.sum(hist_t[L:]) / M
        sig_a = np.var(img[img < bin_edges[L]])
        sig_b = np.var(img[img >= bin_edges[L]])

        within_class_variance = w_a * sig_a + w_b * sig_b
        if within_class_variance < min_var:
            min_var = within_class_variance
            best_threshold = L

    img_t = thresholding(img, best_threshold)
    return img_t, best_threshold

def rgb_to_grayscale(rgb_values):
    rgb = rgb_values
    rgb = rgb.astype(np.uint8)
    rgb_img = Image.fromarray(rgb)
    gray = rgb_img.convert("L")
    return gray

from PIL import Image
def pipeline(X, label, name, m,num, t,n):
    #X = X.apply(pd.to_numeric, errors='coerce')
    if(t!='test'):
        for i in name:
            mm = m+'/' +i
            print(mm)
            files = os.listdir(mm)
            for j in files:
                num +=1
                image_path = mm+ '/'+j
                image = Image.open(image_path)
                q_image = histogram_eq(np.array(image), 256, t)
                qImage = Image.fromarray(q_image)
                qImage.save(image_path) 
                grayscale_image = rgb_to_grayscale(np.array(image))
                image_name = mm+'/'+ str(num) + '_g.jpg'
                grayscale_image.save(image_name) 
        
     
    else:
        for i in name:
            mm = m+'/' +i
            print(mm)
            files = os.listdir(mm)
            for j in files:
                image_path = mm+ '/'+j
                image = Image.open(image_path)
                q_image = histogram_eq(np.array(image), 256, t)
                qImage = Image.fromarray(q_image)
                qImage.save(image_path) 
    
    #plt.imshow(X)
    #return otsu_image, grayscale_image, eq_image, X

#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_m'
#Directories for the training, validation and test splits
train_dir = os.path.join(original_dataset_dir, 'train')
# os.mkdir(train_dir)
validation_dit = os.path.join(original_dataset_dir, 'validation')
# os.mkdir(validation_dit)
test_dir = os.path.join(original_dataset_dir, 'test')
# os.mkdir(test_dir)

train_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True
                                  
                                   #, fill_mode='nearest'
                                   )
test_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True)

# Now, use flow_from_directory without specifying preprocessing_function again

train_generator = train_datagen.flow_from_directory(
    train_dir,
    target_size=(200, 200), # This might be resize () Increase the size. (485-364), yeah change it to square?
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical'
)

    
test_generator = test_datagen.flow_from_directory(
    test_dir,
    target_size=(200, 200),
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical',
    
)

print(type(train_generator))
for data_batch, labels_batch in train_generator:
    print('data batch shape:', data_batch.shape)
    print('labels batch shape:', labels_batch.shape)
    break

#El generador produce lotes de imágenes de tamaño 150x150 (altura y ancho) y 3 (canales de color) y lotes de etiquetas de tamaño 30 (número de imágenes en el lote).

Found 1350 images belonging to 11 classes.
Found 462 images belonging to 11 classes.
<class 'keras.src.preprocessing.image.DirectoryIterator'>
data batch shape: (128, 200, 200, 3)
labels batch shape: (128, 11)

def create_images(generator,m, t):
    name =  os.listdir(m)
    n = generator.filenames
    count = 0
    c = 0
    if t == 'train':
        pipeline(0,0,name,m,count,t,n)
    else:
        pipeline(0,0,name,m,count,t,n)
        
create_images(train_generator,'C:/Users/dggua/Documents/DeepLearning/img_m/train', 'train')  
create_images(test_generator,'C:/Users/dggua/Documents/DeepLearning/img_m/test', 'test')  

C:/Users/dggua/Documents/DeepLearning/img_m/train/actinic_keratosis
357822
393726
695535
480000
478668
241500
393726
168768
2122848
758160
2734155
291225
168768
495768
203550
360138
176256
171072
168768
168768
398088
168192
550800
530640
529620
531783
1131000
529620
529620
529620
529620
529620
529620
336960
530334
530130
572670
529620
527616
530064
529620
567645
164736
473373
673500
537672
558789
631743
168768
393726
165888
808344
421290
168768
165888
864900
507000
165888
464640
504000
471450
165312
679716
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622434
C:/Users/dggua/Documents/DeepLearning/img_m/test/superficial_spreading_melanoma_ssm
1355940
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array([ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  1,  1,
        1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  2,  2,  2,  2,  2,
        2,  2,  2,  2,  2,  2,  2,  2,  2,  2,  2,  2,  3,  3,  3,  3,  3,
        3,  3,  3,  3,  3,  3,  3,  4,  4,  4,  4,  4,  4,  4,  4,  4,  4,
        4,  4,  4,  4,  4,  4,  4,  4,  4,  5,  5,  5,  5,  5,  5,  5,  5,
        5,  5,  5,  5,  5,  5,  5,  5,  5,  5,  5,  5,  6,  6,  6,  6,  6,
        6,  6,  6,  6,  6,  6,  6,  6,  6,  6,  7,  7,  7,  7,  7,  7,  7,
        7,  7,  7,  7,  7,  7,  7,  7,  7,  7,  8,  8,  8,  8,  8,  8,  8,
        8,  8,  8,  8,  8,  8,  8,  8,  8,  8,  8,  8,  8,  9,  9,  9,  9,
        9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
        9,  9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
       10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11,
       11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12,
       12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
       13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
       14, 14, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
       15, 15, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
       16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
       16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
       17, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
       18, 18, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
       19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
       19, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
       20, 20, 20, 20, 20, 20, 20, 20, 20, 21, 21, 21, 21, 21, 21, 21, 21,
       21, 21, 21, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22,
       22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23,
       23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23,
       23, 23, 23, 23, 23, 23, 23, 23])

def delete_images():
    directory = 'C:/Users/dggua/Documents/DeepLearning/img_3/train'

    # List the files in the directory
    files = os.listdir(directory)
    print(files)
    for i in files:
        directory2 = directory+"/"+i
        files2 = os.listdir(directory2)
        for j in files2:
            if ('img' in j):
                file_path = directory2+"/"+j
                os.remove(file_path)

Generators

Color stretching

def channel_stretch(images):
    imagen_flotante = images.astype(np.float64)
    for canal in range(imagen_flotante.shape[2]):
        minimo = np.min(imagen_flotante[:,:,canal])
        maximo = np.max(imagen_flotante[:,:,canal])
        # Aplicar la transformación de estiramiento del contraste
        imagen_flotante[:,:,canal] = (imagen_flotante[:,:,canal] - minimo) / (maximo - minimo) * 255

    images_copy = imagen_flotante.astype(np.uint8)
    return images_copy

def batch_channel_stretch(batch_images):
    # Convert to float to avoid issues with integer overflow/underflow
    batch_images_float = batch_images.astype(np.float64)
    
    for i in range(batch_images_float.shape[0]):  # Iterate over each image in the batch
        for channel in range(batch_images_float.shape[-1]):  # Iterate over each channel
            # Calculate min and max values for the current channel of the current image
            min_val = np.min(batch_images_float[i, :, :, channel])
            max_val = np.max(batch_images_float[i, :, :, channel])
            # Avoid division by zero if the image is constant
            if max_val > min_val:
                # Normalize the current channel of the current image
                batch_images_float[i, :, :, channel] = (batch_images_float[i, :, :, channel] - min_val) / (max_val - min_val) * 255
            else:
                # If max and min are the same, set the channel to zeros (or you might choose 255 for a white image)
                batch_images_float[i, :, :, channel] = np.zeros_like(batch_images_float[i, :, :, channel])
    
    # Convert back to unsigned 8-bit integer type
    return batch_images_float.astype(np.uint8)

img2 = imageio.imread('C:/Users/dggua/Documents/DeepLearning/imgPrueba/melanoma/img1528.jpg')

imagen_final = channel_stretch(img2)

plt.figure(figsize=(20,10))
plt.subplot(131); plt.imshow(img2)
plt.subplot(132); plt.imshow(imagen_final)
plt.show()

C:\Users\dggua\AppData\Local\Temp\ipykernel_1528\3812641245.py:1: DeprecationWarning: Starting with ImageIO v3 the behavior of this function will switch to that of iio.v3.imread. To keep the current behavior (and make this warning disappear) use `import imageio.v2 as imageio` or call `imageio.v2.imread` directly.
  img2 = imageio.imread('C:/Users/dggua/Documents/DeepLearning/imgPrueba/melanoma/img1528.jpg')

## Pre-trained Model VGG16
!pip install keras.applications.vgg16

ERROR: Could not find a version that satisfies the requirement keras.applications.vgg16 (from versions: none)
ERROR: No matching distribution found for keras.applications.vgg16

Color Descriptors

img1 = imageio.imread('C:/Users/dggua/Documents/DeepLearning/imgPrueba/dariers_disease/img145.jpg')
img2 = imageio.imread('C:/Users/dggua/Documents/DeepLearning/imgPrueba/melanoma/img1528.jpg')

plt.figure(figsize=(20,10))
plt.subplot(131) ; plt.imshow(img1[:,:,0], cmap='gray') ; plt.title('RED')
plt.subplot(132) ; plt.imshow(img1[:,:,1], cmap='gray') ; plt.title('GREEN')
plt.subplot(133) ; plt.imshow(img1[:,:,2], cmap='gray') ; plt.title('BLUE')

C:\Users\dggua\AppData\Local\Temp\ipykernel_1528\57107206.py:1: DeprecationWarning: Starting with ImageIO v3 the behavior of this function will switch to that of iio.v3.imread. To keep the current behavior (and make this warning disappear) use `import imageio.v2 as imageio` or call `imageio.v2.imread` directly.
  img1 = imageio.imread('C:/Users/dggua/Documents/DeepLearning/imgPrueba/dariers_disease/img145.jpg')
C:\Users\dggua\AppData\Local\Temp\ipykernel_1528\57107206.py:2: DeprecationWarning: Starting with ImageIO v3 the behavior of this function will switch to that of iio.v3.imread. To keep the current behavior (and make this warning disappear) use `import imageio.v2 as imageio` or call `imageio.v2.imread` directly.
  img2 = imageio.imread('C:/Users/dggua/Documents/DeepLearning/imgPrueba/melanoma/img1528.jpg')

Text(0.5, 1.0, 'BLUE')

Color Stretching Examples

train_images, train_labels = next(train_generator)
validation_images, validation_labels = next(validation_generator)

train_images_stretched = list(map(channel_stretch,train_images))
validation_images_stretched = channel_stretch(validation_images)


plt.figure(figsize=(15,10))
plt.subplot(131); plt.imshow(train_images[10])
plt.subplot(132); plt.imshow(train_images_stretched[10])

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[15], line 2
      1 train_images, train_labels = next(train_generator)
----> 2 validation_images, validation_labels = next(validation_generator)
      4 train_images_stretched = list(map(channel_stretch,train_images))
      5 validation_images_stretched = channel_stretch(validation_images)

NameError: name 'validation_generator' is not defined

Feature Extraction

Step 3 Building the network

def recall_m(y_true, y_pred):
    true_positives = K.sum(K.round(K.clip(y_true * y_pred, 0, 1)))
    possible_positives = K.sum(K.round(K.clip(y_true, 0, 1)))
    recall = true_positives / (possible_positives + K.epsilon())
    return recall

def precision_m(y_true, y_pred):
    true_positives = K.sum(K.round(K.clip(y_true * y_pred, 0, 1)))
    predicted_positives = K.sum(K.round(K.clip(y_pred, 0, 1)))

    precision = true_positives / (predicted_positives + K.epsilon())
    return precision

def f1_m(y_true, y_pred):
    precision = precision_m(y_true, y_pred)
    recall = recall_m(y_true, y_pred)
    return 2*((precision*recall)/(precision+recall+K.epsilon()))

def f1_weighted(true, pred): #shapes (batch, 4)

    #for metrics include these two lines, for loss, don't include them
    #these are meant to round 'pred' to exactly zeros and ones
    #predLabels = K.argmax(pred, axis=-1)
    #pred = K.one_hot(predLabels, 4) 


    ground_positives = K.sum(true, axis=0) + K.epsilon()       # = TP + FN
    pred_positives = K.sum(pred, axis=0) + K.epsilon()         # = TP + FP
    true_positives = K.sum(true * pred, axis=0) + K.epsilon()  # = TP
        #all with shape (4,)
    
    precision = true_positives / pred_positives 
    recall = true_positives / ground_positives
        #both = 1 if ground_positives == 0 or pred_positives == 0
        #shape (4,)

    f1 = 2 * (precision * recall) / (precision + recall + K.epsilon())
        #still with shape (4,)

    weighted_f1 = f1 * ground_positives / K.sum(ground_positives) 
    weighted_f1 = K.sum(weighted_f1)

    
    return 1 - weighted_f1

#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_3'
#Directories for the training, validation and test splits
train_dir = os.path.join(original_dataset_dir, 'train')
# os.mkdir(train_dir)
validation_dit = os.path.join(original_dataset_dir, 'validation')
# os.mkdir(validation_dit)
test_dir = os.path.join(original_dataset_dir, 'test')
# os.mkdir(test_dir)

train_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True
                                  
                                   #, fill_mode='nearest'
                                   )
test_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True)

# Now, use flow_from_directory without specifying preprocessing_function again

train_generator = train_datagen.flow_from_directory(
    train_dir,
    target_size=(200, 200), # This might be resize () Increase the size. (485-364), yeah change it to square?
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical'
)

    
validation_generator = test_datagen.flow_from_directory(
    validation_dit,
    target_size=(200, 200),
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical',
    
)

print(type(train_generator))
for data_batch, labels_batch in train_generator:
    print('data batch shape:', data_batch.shape)
    print('labels batch shape:', labels_batch.shape)
    break

#El generador produce lotes de imágenes de tamaño 150x150 (altura y ancho) y 3 (canales de color) y lotes de etiquetas de tamaño 30 (número de imágenes en el lote).

Found 19730 images belonging to 3 classes.
Found 3260 images belonging to 3 classes.
<class 'keras.src.preprocessing.image.DirectoryIterator'>
data batch shape: (128, 200, 200, 3)
labels batch shape: (128, 3)

IMG_SIZE = 200

resize_and_rescale = Sequential([
  layers.Resizing(IMG_SIZE, IMG_SIZE),
  layers.Rescaling(1./255)
])
data_augmentation = Sequential([
  layers.RandomFlip("horizontal_and_vertical"),
  layers.RandomRotation(0.4),
])

WARNING:tensorflow:From C:\Users\dggua\anaconda3\Lib\site-packages\keras\src\backend.py:873: The name tf.get_default_graph is deprecated. Please use tf.compat.v1.get_default_graph instead.

IMG_SIZE = 200
model = models.Sequential([
  layers.Resizing(IMG_SIZE, IMG_SIZE),
  layers.Rescaling(1./255)
])
model = models.Sequential([
  layers.RandomFlip("horizontal_and_vertical"),
  layers.RandomRotation(0.4),
])
model.add(layers.Conv2D(32, (3, 3), activation='relu', input_shape=(50, 50, 3)))
model.add(layers.MaxPooling2D((2, 2)))
model.add(layers.Conv2D(64, (3, 3), activation='relu'))
model.add(layers.MaxPooling2D((2, 2)))
model.add(layers.Conv2D(128, (3, 3), activation='relu'))
    #model.add(layers.MaxPooling2D((2, 2)))
model.add(layers.Conv2D(128, (3, 3), activation='relu'))
model.add(layers.MaxPooling2D((2, 2)))
model.add(layers.Flatten())
model.add(layers.Dropout(0.5))
model.add(layers.Dense(512, activation='relu'))
model.add(layers.Dense(3, activation='softmax'))  # Output layer with 114 units and sigmoid activation

model.compile(optimizer=optimizers.RMSprop(lr=1e-4),
                  loss='categorical_crossentropy',
                  metrics=['accuracy','Precision','Recall',f1_m,f1_weighted])

WARNING:tensorflow:From C:\Users\dggua\anaconda3\Lib\site-packages\keras\src\layers\pooling\max_pooling2d.py:161: The name tf.nn.max_pool is deprecated. Please use tf.nn.max_pool2d instead.

WARNING:absl:`lr` is deprecated in Keras optimizer, please use `learning_rate` or use the legacy optimizer, e.g.,tf.keras.optimizers.legacy.RMSprop.

history = model.fit_generator(
    train_generator,
    steps_per_epoch=train_generator.n//train_generator.batch_size,
    epochs=10,
    validation_data=validation_generator,
    validation_steps=validation_generator.n//validation_generator.batch_size
)

model.save('Dermatology_problem_v1.h5')

C:\Users\dggua\AppData\Local\Temp\ipykernel_20580\1661183745.py:1: UserWarning: `Model.fit_generator` is deprecated and will be removed in a future version. Please use `Model.fit`, which supports generators.
  history = model.fit_generator(

Epoch 1/10
WARNING:tensorflow:From C:\Users\dggua\anaconda3\Lib\site-packages\keras\src\utils\tf_utils.py:492: The name tf.ragged.RaggedTensorValue is deprecated. Please use tf.compat.v1.ragged.RaggedTensorValue instead.

WARNING:tensorflow:From C:\Users\dggua\anaconda3\Lib\site-packages\keras\src\utils\tf_utils.py:492: The name tf.ragged.RaggedTensorValue is deprecated. Please use tf.compat.v1.ragged.RaggedTensorValue instead.

WARNING:tensorflow:From C:\Users\dggua\anaconda3\Lib\site-packages\keras\src\engine\base_layer_utils.py:384: The name tf.executing_eagerly_outside_functions is deprecated. Please use tf.compat.v1.executing_eagerly_outside_functions instead.

WARNING:tensorflow:From C:\Users\dggua\anaconda3\Lib\site-packages\keras\src\engine\base_layer_utils.py:384: The name tf.executing_eagerly_outside_functions is deprecated. Please use tf.compat.v1.executing_eagerly_outside_functions instead.

154/154 [==============================] - 1686s 11s/step - loss: 1.0476 - accuracy: 0.7206 - precision: 0.7291 - recall: 0.6933 - f1_m: 0.6930 - f1_weighted: 0.4464 - val_loss: 0.7669 - val_accuracy: 0.7303 - val_precision: 0.7303 - val_recall: 0.7303 - val_f1_m: 0.7303 - val_f1_weighted: 0.4336
Epoch 2/10
154/154 [==============================] - 1450s 9s/step - loss: 0.7674 - accuracy: 0.7288 - precision: 0.7330 - recall: 0.7219 - f1_m: 0.7263 - f1_weighted: 0.4269 - val_loss: 0.7551 - val_accuracy: 0.7275 - val_precision: 0.7284 - val_recall: 0.7275 - val_f1_m: 0.7280 - val_f1_weighted: 0.4268
Epoch 3/10
154/154 [==============================] - 1453s 9s/step - loss: 0.7585 - accuracy: 0.7298 - precision: 0.7362 - recall: 0.7193 - f1_m: 0.7260 - f1_weighted: 0.4234 - val_loss: 0.7542 - val_accuracy: 0.7284 - val_precision: 0.7303 - val_recall: 0.7278 - val_f1_m: 0.7290 - val_f1_weighted: 0.4153
Epoch 4/10
154/154 [==============================] - 1471s 10s/step - loss: 0.7514 - accuracy: 0.7293 - precision: 0.7370 - recall: 0.7178 - f1_m: 0.7272 - f1_weighted: 0.4182 - val_loss: 0.7560 - val_accuracy: 0.7334 - val_precision: 0.7440 - val_recall: 0.7138 - val_f1_m: 0.7285 - val_f1_weighted: 0.4379
Epoch 5/10
154/154 [==============================] - 1449s 9s/step - loss: 0.7493 - accuracy: 0.7306 - precision: 0.7395 - recall: 0.7166 - f1_m: 0.7266 - f1_weighted: 0.4172 - val_loss: 0.7449 - val_accuracy: 0.7309 - val_precision: 0.7330 - val_recall: 0.7250 - val_f1_m: 0.7289 - val_f1_weighted: 0.4229
Epoch 6/10
154/154 [==============================] - 1462s 9s/step - loss: 0.7439 - accuracy: 0.7315 - precision: 0.7422 - recall: 0.7124 - f1_m: 0.7269 - f1_weighted: 0.4140 - val_loss: 0.7411 - val_accuracy: 0.7294 - val_precision: 0.7419 - val_recall: 0.7169 - val_f1_m: 0.7291 - val_f1_weighted: 0.4247
Epoch 7/10
154/154 [==============================] - 1442s 9s/step - loss: 0.7388 - accuracy: 0.7340 - precision: 0.7451 - recall: 0.7148 - f1_m: 0.7290 - f1_weighted: 0.4113 - val_loss: 0.7286 - val_accuracy: 0.7344 - val_precision: 0.7441 - val_recall: 0.7241 - val_f1_m: 0.7339 - val_f1_weighted: 0.4047
Epoch 8/10
154/154 [==============================] - 1450s 9s/step - loss: 0.7341 - accuracy: 0.7340 - precision: 0.7471 - recall: 0.7131 - f1_m: 0.7294 - f1_weighted: 0.4087 - val_loss: 0.7335 - val_accuracy: 0.7366 - val_precision: 0.7433 - val_recall: 0.7247 - val_f1_m: 0.7339 - val_f1_weighted: 0.3971
Epoch 9/10
154/154 [==============================] - 1446s 9s/step - loss: 0.7281 - accuracy: 0.7356 - precision: 0.7492 - recall: 0.7135 - f1_m: 0.7293 - f1_weighted: 0.4063 - val_loss: 0.7405 - val_accuracy: 0.7297 - val_precision: 0.7363 - val_recall: 0.7278 - val_f1_m: 0.7320 - val_f1_weighted: 0.3995
Epoch 10/10
154/154 [==============================] - 1439s 9s/step - loss: 0.7280 - accuracy: 0.7354 - precision: 0.7506 - recall: 0.7116 - f1_m: 0.7301 - f1_weighted: 0.4043 - val_loss: 0.7354 - val_accuracy: 0.7372 - val_precision: 0.7464 - val_recall: 0.7212 - val_f1_m: 0.7337 - val_f1_weighted: 0.3893

C:\Users\dggua\anaconda3\Lib\site-packages\keras\src\engine\training.py:3103: UserWarning: You are saving your model as an HDF5 file via `model.save()`. This file format is considered legacy. We recommend using instead the native Keras format, e.g. `model.save('my_model.keras')`.
  saving_api.save_model(

Step 3 Model Fitting

Identify corrupted image files

def delete_corrpted_images():
#Images corrupted image files, unsupported image formats, or incorrect file paths 

 for label in labels:
    label_dir = os.path.join(validation_dit, label)
    for fname in os.listdir(label_dir):
        try:
            img = cv2.imread(os.path.join(label_dir, fname))
            if img is None:
                print('File {} is not a valid image file'.format(fname), label)
        except:
            print('File {} is not a valid image file'.format(fname), label)

#tf.keras.backend.clear_session()

Step 4 Plot metrics

def Plot_Metrics():
    #Now we will plot the training and validation accuracy and loss
    metric = 'accuracy' #sensitivity, specificity, precision, recall, f1-score can also be used
    acc = history.history[metric]
    val_acc = history.history['val_accuracy']
    loss = history.history['loss']
    val_loss = history.history['val_loss']

    epochs = range(1, len(acc) + 1)

    plt.plot(epochs, acc, 'bo', label='Training acc')
    plt.plot(epochs, val_acc, 'b', label='Validation acc')
    plt.title('Training and validation accuracy')
    plt.legend()

    plt.figure()

    plt.plot(epochs, loss, 'bo', label='Training loss')
    plt.plot(epochs, val_loss, 'b', label='Validation loss')
    plt.title('Training and validation loss')
    plt.legend()

    plt.show()
    print(test_datagen)
    #Now we will evaluate the model on the test set
    #test_loss, test_acc = model.evaluate_generator(test_datagen, steps=50)
    #print('test acc:', test_acc)

    #Now we will make predictions on the test set
    predictions = model.predict_generator(validation_generator, steps=50)
    print(predictions)

Run the first Model to check the results

#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_3'
#Directories for the training, validation and test splits
train_dir = os.path.join(original_dataset_dir, 'train')
# os.mkdir(train_dir)
validation_dit = os.path.join(original_dataset_dir, 'validation')
# os.mkdir(validation_dit)
test_dir = os.path.join(original_dataset_dir, 'test')
# os.mkdir(test_dir)

train_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True
                                  
                                   #, fill_mode='nearest'
                                   )
test_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True)

# Now, use flow_from_directory without specifying preprocessing_function again

train_generator = train_datagen.flow_from_directory(
    train_dir,
    target_size=(200, 200), # This might be resize () Increase the size. (485-364), yeah change it to square?
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical'
)

    
validation_generator = test_datagen.flow_from_directory(
    validation_dit,
    target_size=(200, 200),
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical',
    
)

print(type(train_generator))
for data_batch, labels_batch in train_generator:
    print('data batch shape:', data_batch.shape)
    print('labels batch shape:', labels_batch.shape)
    break

#El generador produce lotes de imágenes de tamaño 150x150 (altura y ancho) y 3 (canales de color) y lotes de etiquetas de tamaño 30 (número de imágenes en el lote).

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[1], line 4
      2 original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_3'
      3 #Directories for the training, validation and test splits
----> 4 train_dir = os.path.join(original_dataset_dir, 'train')
      5 # os.mkdir(train_dir)
      6 validation_dit = os.path.join(original_dataset_dir, 'validation')

NameError: name 'os' is not defined

#Creating Predictions
predictions = model.predict_generator(test_generator,  verbose = 1)

C:\Users\dggua\AppData\Local\Temp\ipykernel_10776\846870615.py:2: UserWarning: `Model.predict_generator` is deprecated and will be removed in a future version. Please use `Model.predict`, which supports generators.
  predictions = model.predict_generator(test_generator,  verbose = 1)

27/27 [==============================] - 188s 7s/step

predictions[0]

array([0.18996486, 0.59574866, 0.21428649], dtype=float32)

#Checking how many rights and wrongs prediction we got
points = 0
points_w = 0
c = 0
class_indices = train_generator.classes
at = []
for i in predictions: 
    random_num = round(random.uniform(0, 1), 8)
    classi = 0
    if(random_num <= i[0]):
        classi = 0
    elif((random_num > i[0]) and (random_num<=(i[1]+i[0]))):
        classi = 1
    else:
        classi = 2
    if(classi==class_indices[c]):
        points+=1
        at.append(classi)
    else:
        points_w+=1
        at.append(4)
    c+=1

print(points, points_w)
print(points/(points+points_w))
print(Counter(at))
print(Counter(class_indices))

849 2552
0.24963246104087033
Counter({4: 2552, 1: 502, 0: 347})
Counter({1: 14374, 0: 2700, 2: 2656})

Run the Models for belign, Malignant and non-neoplastic

take in mind if there is a problem please run:

#### tf.keras.backend.clear_session()

tf.keras.backend.clear_session()

#This is the directory where the images are stored 
dw_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/imgPrueba'

#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_b'
#Directories for the training, validation and test splits
train_dir = os.path.join(original_dataset_dir, 'train')
# os.mkdir(train_dir)
validation_dit = os.path.join(original_dataset_dir, 'validation')
# os.mkdir(validation_dit)
test_dir = os.path.join(original_dataset_dir, 'test')
# os.mkdir(test_dir)

#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_b'
#Directories for the training, validation and test splits
train_dir = os.path.join(original_dataset_dir, 'train')
# os.mkdir(train_dir)
validation_dit = os.path.join(original_dataset_dir, 'validation')
# os.mkdir(validation_dit)
test_dir = os.path.join(original_dataset_dir, 'test')
# os.mkdir(test_dir)

train_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True
                                  
                                   #, fill_mode='nearest'
                                   )
test_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True)

# Now, use flow_from_directory without specifying preprocessing_function again

train_generator = train_datagen.flow_from_directory(
    train_dir,
    target_size=(200, 200), # This might be resize () Increase the size. (485-364), yeah change it to square?
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical'
)

    
validation_generator = test_datagen.flow_from_directory(
    validation_dit,
    target_size=(200, 200),
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical',
    
)

print(type(train_generator))
for data_batch, labels_batch in train_generator:
    print('data batch shape:', data_batch.shape)
    print('labels batch shape:', labels_batch.shape)
    break

#El generador produce lotes de imágenes de tamaño 150x150 (altura y ancho) y 3 (canales de color) y lotes de etiquetas de tamaño 30 (número de imágenes en el lote).

Found 2656 images belonging to 24 classes.
Found 436 images belonging to 24 classes.
<class 'keras.src.preprocessing.image.DirectoryIterator'>
data batch shape: (128, 200, 200, 3)
labels batch shape: (128, 24)

train_generator.class_indices.keys()

dict_keys(['becker_nevus', 'congenital_nevus', 'dermatofibroma', 'disseminated_actinic_porokeratosis', 'epidermal_nevus', 'fordyce_spots', 'granuloma_pyogenic', 'halo_nevus', 'lymphangioma', 'milia', 'mucous_cyst', 'naevus_comedonicus', 'nevocytic_nevus', 'nevus_sebaceous_of_jadassohn', 'pilar_cyst', 'pilomatricoma', 'porokeratosis_actinic', 'porokeratosis_of_mibelli', 'port_wine_stain', 'prurigo_nodularis', 'pyogenic_granuloma', 'seborrheic_keratosis', 'syringoma', 'telangiectases'])

IMG_SIZE = 200
model2 = models.Sequential([
  layers.Resizing(IMG_SIZE, IMG_SIZE),
  layers.Rescaling(1./255)
])
model2 = models.Sequential([
  layers.RandomFlip("horizontal_and_vertical"),
  layers.RandomRotation(0.4),
])
model2.add(layers.Conv2D(32, (3, 3), activation='relu', input_shape=(200, 200, 3)))
model2.add(layers.MaxPooling2D((2, 2)))
model2.add(layers.Conv2D(64, (3, 3), activation='relu'))
model2.add(layers.MaxPooling2D((2, 2)))
model2.add(layers.Conv2D(128, (3, 3), activation='relu'))
    #model.add(layers.MaxPooling2D((2, 2)))
model2.add(layers.Conv2D(128, (3, 3), activation='relu'))
model2.add(layers.MaxPooling2D((2, 2)))
model2.add(layers.Flatten())
model2.add(layers.Dropout(0.5))
model2.add(layers.Dense(512, activation='relu'))
model2.add(layers.Dense(24, activation='softmax'))  # Output layer with 114 units and sigmoid activation

model2.compile(optimizer=optimizers.RMSprop(lr=1e-4),
                  loss='categorical_crossentropy',
                  metrics=['accuracy','Precision','Recall',f1_m,f1_weighted])

WARNING:absl:`lr` is deprecated in Keras optimizer, please use `learning_rate` or use the legacy optimizer, e.g.,tf.keras.optimizers.legacy.RMSprop.

history = model2.fit_generator(
    train_generator,
    steps_per_epoch=train_generator.n//train_generator.batch_size,
    epochs=20,
    validation_data=validation_generator,
    validation_steps=validation_generator.n//validation_generator.batch_size
)

model2.save('Dermatology_problem_v1_b.h5')

C:\Users\dggua\AppData\Local\Temp\ipykernel_20580\2294588897.py:1: UserWarning: `Model.fit_generator` is deprecated and will be removed in a future version. Please use `Model.fit`, which supports generators.
  history = model2.fit_generator(

Epoch 1/20
20/20 [==============================] - 224s 11s/step - loss: 3.6800 - accuracy: 0.0653 - precision: 0.0547 - recall: 0.0028 - f1_m: 0.0027 - f1_weighted: 0.9557 - val_loss: 3.1281 - val_accuracy: 0.0703 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9527
Epoch 2/20
20/20 [==============================] - 190s 9s/step - loss: 3.1418 - accuracy: 0.0783 - precision: 0.0000e+00 - recall: 0.0000e+00 - f1_m: 0.0000e+00 - f1_weighted: 0.9521 - val_loss: 3.1317 - val_accuracy: 0.0703 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9527
Epoch 3/20
20/20 [==============================] - 184s 9s/step - loss: 3.1360 - accuracy: 0.0803 - precision: 0.0000e+00 - recall: 0.0000e+00 - f1_m: 0.0000e+00 - f1_weighted: 0.9516 - val_loss: 3.1112 - val_accuracy: 0.0755 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9515
Epoch 4/20
20/20 [==============================] - 183s 9s/step - loss: 3.1162 - accuracy: 0.0866 - precision: 0.0000e+00 - recall: 0.0000e+00 - f1_m: 0.0000e+00 - f1_weighted: 0.9495 - val_loss: 3.1213 - val_accuracy: 0.0729 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9515
Epoch 5/20
20/20 [==============================] - 183s 9s/step - loss: 3.1183 - accuracy: 0.0878 - precision: 0.0000e+00 - recall: 0.0000e+00 - f1_m: 0.0000e+00 - f1_weighted: 0.9498 - val_loss: 3.0969 - val_accuracy: 0.0911 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9506
Epoch 6/20
20/20 [==============================] - 183s 9s/step - loss: 3.1115 - accuracy: 0.0996 - precision: 0.2857 - recall: 7.8125e-04 - f1_m: 0.0015 - f1_weighted: 0.9486 - val_loss: 3.0758 - val_accuracy: 0.0911 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9496
Epoch 7/20
20/20 [==============================] - 201s 10s/step - loss: 3.0673 - accuracy: 0.1036 - precision: 0.2000 - recall: 3.9557e-04 - f1_m: 7.5758e-04 - f1_weighted: 0.9452 - val_loss: 4.4223 - val_accuracy: 0.0234 - val_precision: 0.0427 - val_recall: 0.0234 - val_f1_m: 0.0305 - val_f1_weighted: 0.9730
Epoch 8/20
20/20 [==============================] - 330s 16s/step - loss: 3.1310 - accuracy: 0.0989 - precision: 0.0769 - recall: 0.0016 - f1_m: 0.0025 - f1_weighted: 0.9459 - val_loss: 3.0750 - val_accuracy: 0.0885 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9474
Epoch 9/20
20/20 [==============================] - 184s 9s/step - loss: 3.0497 - accuracy: 0.1112 - precision: 0.0000e+00 - recall: 0.0000e+00 - f1_m: 0.0000e+00 - f1_weighted: 0.9413 - val_loss: 3.0215 - val_accuracy: 0.1406 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9449
Epoch 10/20
20/20 [==============================] - 184s 9s/step - loss: 3.0020 - accuracy: 0.1353 - precision: 0.3125 - recall: 0.0020 - f1_m: 0.0035 - f1_weighted: 0.9374 - val_loss: 2.9877 - val_accuracy: 0.1250 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9400
Epoch 11/20
20/20 [==============================] - 184s 9s/step - loss: 2.9799 - accuracy: 0.1218 - precision: 0.1667 - recall: 0.0012 - f1_m: 0.0022 - f1_weighted: 0.9348 - val_loss: 3.0206 - val_accuracy: 0.1146 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9388
Epoch 12/20
20/20 [==============================] - 182s 9s/step - loss: 2.9826 - accuracy: 0.1262 - precision: 0.6667 - recall: 0.0040 - f1_m: 0.0077 - f1_weighted: 0.9345 - val_loss: 2.9905 - val_accuracy: 0.1172 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9385
Epoch 13/20
20/20 [==============================] - 184s 9s/step - loss: 2.9474 - accuracy: 0.1499 - precision: 0.3333 - recall: 0.0028 - f1_m: 0.0052 - f1_weighted: 0.9303 - val_loss: 2.9537 - val_accuracy: 0.1276 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9370
Epoch 14/20
20/20 [==============================] - 182s 9s/step - loss: 2.9267 - accuracy: 0.1420 - precision: 0.4167 - recall: 0.0020 - f1_m: 0.0038 - f1_weighted: 0.9284 - val_loss: 2.9504 - val_accuracy: 0.1458 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9379
Epoch 15/20
20/20 [==============================] - 183s 9s/step - loss: 2.9132 - accuracy: 0.1602 - precision: 0.2500 - recall: 0.0036 - f1_m: 0.0067 - f1_weighted: 0.9246 - val_loss: 2.9760 - val_accuracy: 0.1172 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9357
Epoch 16/20
20/20 [==============================] - 183s 9s/step - loss: 2.8798 - accuracy: 0.1594 - precision: 0.4324 - recall: 0.0063 - f1_m: 0.0121 - f1_weighted: 0.9208 - val_loss: 2.9440 - val_accuracy: 0.1224 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9355
Epoch 17/20
20/20 [==============================] - 186s 9s/step - loss: 2.8666 - accuracy: 0.1638 - precision: 0.3750 - recall: 0.0036 - f1_m: 0.0069 - f1_weighted: 0.9201 - val_loss: 2.8910 - val_accuracy: 0.1771 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9238
Epoch 18/20
20/20 [==============================] - 183s 9s/step - loss: 2.8467 - accuracy: 0.1776 - precision: 0.4423 - recall: 0.0091 - f1_m: 0.0175 - f1_weighted: 0.9155 - val_loss: 2.9009 - val_accuracy: 0.1510 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9281
Epoch 19/20
20/20 [==============================] - 183s 9s/step - loss: 2.8216 - accuracy: 0.1764 - precision: 0.3750 - recall: 0.0071 - f1_m: 0.0137 - f1_weighted: 0.9127 - val_loss: 2.8941 - val_accuracy: 0.1432 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9285
Epoch 20/20
20/20 [==============================] - 182s 9s/step - loss: 2.8047 - accuracy: 0.1784 - precision: 0.4500 - recall: 0.0142 - f1_m: 0.0271 - f1_weighted: 0.9098 - val_loss: 2.8531 - val_accuracy: 0.1615 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9234

#This is the directory where the images are stored 
dw_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/imgPrueba'

#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_n'
#Directories for the training, validation and test splits
train_dir = os.path.join(original_dataset_dir, 'train')
# os.mkdir(train_dir)
validation_dit = os.path.join(original_dataset_dir, 'validation')
# os.mkdir(validation_dit)
test_dir = os.path.join(original_dataset_dir, 'test')
# os.mkdir(test_dir)

train_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True
                                  
                                   #, fill_mode='nearest'
                                   )
test_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True)

# Now, use flow_from_directory without specifying preprocessing_function again

train_generator = train_datagen.flow_from_directory(
    train_dir,
    target_size=(200, 200), # This might be resize () Increase the size. (485-364), yeah change it to square?
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical'
)

    
validation_generator = test_datagen.flow_from_directory(
    validation_dit,
    target_size=(200, 200),
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical',
    
)

print(type(train_generator))
for data_batch, labels_batch in train_generator:
    print('data batch shape:', data_batch.shape)
    print('labels batch shape:', labels_batch.shape)
    break

Found 14374 images belonging to 79 classes.
Found 2376 images belonging to 79 classes.
<class 'keras.src.preprocessing.image.DirectoryIterator'>
data batch shape: (128, 200, 200, 3)
labels batch shape: (128, 79)

IMG_SIZE = 200
model3 = models.Sequential([
  layers.Resizing(IMG_SIZE, IMG_SIZE),
  layers.Rescaling(1./255)
])
model3 = models.Sequential([
  layers.RandomFlip("horizontal_and_vertical"),
  layers.RandomRotation(0.4),
])
model3.add(layers.Conv2D(32, (3, 3), activation='relu', input_shape=(200, 200, 3)))
model3.add(layers.MaxPooling2D((2, 2)))
model3.add(layers.Conv2D(64, (3, 3), activation='relu'))
model3.add(layers.MaxPooling2D((2, 2)))
model3.add(layers.Conv2D(128, (3, 3), activation='relu'))
    #model.add(layers.MaxPooling2D((2, 2)))
model3.add(layers.Conv2D(128, (3, 3), activation='relu'))
model3.add(layers.MaxPooling2D((2, 2)))
model3.add(layers.Flatten())
model3.add(layers.Dropout(0.5))
model3.add(layers.Dense(512, activation='relu'))
model3.add(layers.Dense(79, activation='softmax'))  # Output layer with 114 units and sigmoid activation

model3.compile(optimizer=optimizers.RMSprop(lr=1e-4),
                  loss='categorical_crossentropy',
                  metrics=['accuracy','Precision','Recall',f1_m,f1_weighted])

WARNING:absl:`lr` is deprecated in Keras optimizer, please use `learning_rate` or use the legacy optimizer, e.g.,tf.keras.optimizers.legacy.RMSprop.

history3 = model3.fit_generator(
    train_generator,
    steps_per_epoch=train_generator.n//train_generator.batch_size,
    epochs=15,
    validation_data=validation_generator,
    validation_steps=validation_generator.n//validation_generator.batch_size
)

model3.save('Dermatology_problem_v1_n.h5')

C:\Users\dggua\AppData\Local\Temp\ipykernel_20580\494932761.py:1: UserWarning: `Model.fit_generator` is deprecated and will be removed in a future version. Please use `Model.fit`, which supports generators.
  history3 = model3.fit_generator(

Epoch 1/15
112/112 [==============================] - 1212s 11s/step - loss: 4.2005 - accuracy: 0.0523 - precision: 0.0000e+00 - recall: 0.0000e+00 - f1_m: 0.0000e+00 - f1_weighted: 0.9790 - val_loss: 4.1395 - val_accuracy: 0.0556 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9775
Epoch 2/15
112/112 [==============================] - 1034s 9s/step - loss: 4.1505 - accuracy: 0.0543 - precision: 0.0000e+00 - recall: 0.0000e+00 - f1_m: 0.0000e+00 - f1_weighted: 0.9782 - val_loss: 4.1668 - val_accuracy: 0.0556 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9797
Epoch 3/15
112/112 [==============================] - 1027s 9s/step - loss: 4.1361 - accuracy: 0.0537 - precision: 0.0000e+00 - recall: 0.0000e+00 - f1_m: 0.0000e+00 - f1_weighted: 0.9777 - val_loss: 4.1181 - val_accuracy: 0.0516 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9778
Epoch 4/15
112/112 [==============================] - 1024s 9s/step - loss: 4.0842 - accuracy: 0.0597 - precision: 0.0000e+00 - recall: 0.0000e+00 - f1_m: 0.0000e+00 - f1_weighted: 0.9756 - val_loss: 4.0504 - val_accuracy: 0.0551 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9738
Epoch 5/15
112/112 [==============================] - 1136s 10s/step - loss: 4.0385 - accuracy: 0.0623 - precision: 0.1429 - recall: 7.0195e-05 - f1_m: 1.3843e-04 - f1_weighted: 0.9734 - val_loss: 4.0665 - val_accuracy: 0.0499 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9746
Epoch 6/15
112/112 [==============================] - 1054s 9s/step - loss: 3.9974 - accuracy: 0.0691 - precision: 0.1250 - recall: 7.0195e-05 - f1_m: 1.3736e-04 - f1_weighted: 0.9717 - val_loss: 3.9897 - val_accuracy: 0.0681 - val_precision: 0.5000 - val_recall: 8.6806e-04 - val_f1_m: 0.0017 - val_f1_weighted: 0.9680
Epoch 7/15
112/112 [==============================] - 1053s 9s/step - loss: 3.9618 - accuracy: 0.0737 - precision: 0.5385 - recall: 9.8273e-04 - f1_m: 0.0019 - f1_weighted: 0.9692 - val_loss: 3.9465 - val_accuracy: 0.0642 - val_precision: 0.3784 - val_recall: 0.0061 - val_f1_m: 0.0118 - val_f1_weighted: 0.9662
Epoch 8/15
112/112 [==============================] - 1230s 11s/step - loss: 3.9167 - accuracy: 0.0817 - precision: 0.5439 - recall: 0.0022 - f1_m: 0.0043 - f1_weighted: 0.9664 - val_loss: 3.9646 - val_accuracy: 0.0738 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9704
Epoch 9/15
112/112 [==============================] - 1052s 9s/step - loss: 3.8753 - accuracy: 0.0833 - precision: 0.5781 - recall: 0.0026 - f1_m: 0.0051 - f1_weighted: 0.9637 - val_loss: 3.8977 - val_accuracy: 0.0890 - val_precision: 0.5833 - val_recall: 0.0030 - val_f1_m: 0.0060 - val_f1_weighted: 0.9633
Epoch 10/15
112/112 [==============================] - 1063s 9s/step - loss: 3.8242 - accuracy: 0.0940 - precision: 0.6042 - recall: 0.0041 - f1_m: 0.0079 - f1_weighted: 0.9604 - val_loss: 3.8554 - val_accuracy: 0.0872 - val_precision: 0.4615 - val_recall: 0.0052 - val_f1_m: 0.0103 - val_f1_weighted: 0.9610
Epoch 11/15
112/112 [==============================] - 1092s 10s/step - loss: 3.7782 - accuracy: 0.0997 - precision: 0.5250 - recall: 0.0044 - f1_m: 0.0086 - f1_weighted: 0.9571 - val_loss: 3.9315 - val_accuracy: 0.0877 - val_precision: 0.6154 - val_recall: 0.0035 - val_f1_m: 0.0069 - val_f1_weighted: 0.9575
Epoch 12/15
112/112 [==============================] - 1057s 9s/step - loss: 3.7343 - accuracy: 0.1061 - precision: 0.6567 - recall: 0.0062 - f1_m: 0.0121 - f1_weighted: 0.9534 - val_loss: 3.7813 - val_accuracy: 0.1072 - val_precision: 0.5143 - val_recall: 0.0078 - val_f1_m: 0.0153 - val_f1_weighted: 0.9524
Epoch 13/15
112/112 [==============================] - 1056s 9s/step - loss: 3.6911 - accuracy: 0.1135 - precision: 0.6183 - recall: 0.0081 - f1_m: 0.0160 - f1_weighted: 0.9498 - val_loss: 3.8485 - val_accuracy: 0.0972 - val_precision: 0.5789 - val_recall: 0.0095 - val_f1_m: 0.0186 - val_f1_weighted: 0.9514
Epoch 14/15
112/112 [==============================] - 1057s 9s/step - loss: 3.6539 - accuracy: 0.1233 - precision: 0.5917 - recall: 0.0070 - f1_m: 0.0143 - f1_weighted: 0.9465 - val_loss: 3.7569 - val_accuracy: 0.1146 - val_precision: 0.5490 - val_recall: 0.0122 - val_f1_m: 0.0236 - val_f1_weighted: 0.9480
Epoch 15/15
112/112 [==============================] - 1052s 9s/step - loss: 3.6154 - accuracy: 0.1249 - precision: 0.6540 - recall: 0.0097 - f1_m: 0.0191 - f1_weighted: 0.9431 - val_loss: 3.7614 - val_accuracy: 0.0951 - val_precision: 0.7000 - val_recall: 0.0091 - val_f1_m: 0.0179 - val_f1_weighted: 0.9485

#This is the directory where the images are stored 
dw_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/imgPrueba'

#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_m'
#Directories for the training, validation and test splits
train_dir = os.path.join(original_dataset_dir, 'train')
# os.mkdir(train_dir)
validation_dit = os.path.join(original_dataset_dir, 'validation')
# os.mkdir(validation_dit)
test_dir = os.path.join(original_dataset_dir, 'test')
# os.mkdir(test_dir)
    

train_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True
                                  
                                   #, fill_mode='nearest'
                                   )
test_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True)

# Now, use flow_from_directory without specifying preprocessing_function again

train_generator = train_datagen.flow_from_directory(
    train_dir,
    target_size=(200, 200), # This might be resize () Increase the size. (485-364), yeah change it to square?
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical'
)

    
validation_generator = test_datagen.flow_from_directory(
    validation_dit,
    target_size=(200, 200),
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical',
    
)

print(type(train_generator))
for data_batch, labels_batch in train_generator:
    print('data batch shape:', data_batch.shape)
    print('labels batch shape:', labels_batch.shape)
    break

Found 2700 images belonging to 11 classes.
Found 448 images belonging to 11 classes.
<class 'keras.src.preprocessing.image.DirectoryIterator'>
data batch shape: (128, 200, 200, 3)
labels batch shape: (128, 11)

IMG_SIZE = 200
model4 = models.Sequential([
  layers.Resizing(IMG_SIZE, IMG_SIZE),
  layers.Rescaling(1./255)
])
model4 = models.Sequential([
  layers.RandomFlip("horizontal_and_vertical"),
  layers.RandomRotation(0.4),
])
model4.add(layers.Conv2D(32, (3, 3), activation='relu', input_shape=(200, 200, 3)))
model4.add(layers.MaxPooling2D((2, 2)))
model4.add(layers.Conv2D(64, (3, 3), activation='relu'))
model4.add(layers.MaxPooling2D((2, 2)))
model4.add(layers.Conv2D(128, (3, 3), activation='relu'))
    #model.add(layers.MaxPooling2D((2, 2)))
model4.add(layers.Conv2D(128, (3, 3), activation='relu'))
model4.add(layers.MaxPooling2D((2, 2)))
model4.add(layers.Flatten())
model4.add(layers.Dropout(0.5))
model4.add(layers.Dense(512, activation='relu'))
model4.add(layers.Dense(11, activation='softmax'))  # Output layer with 114 units and sigmoid activation

model4.compile(optimizer=optimizers.RMSprop(lr=1e-4),
                  loss='categorical_crossentropy',
                  metrics=['accuracy','Precision','Recall',f1_m,f1_weighted])

WARNING:absl:`lr` is deprecated in Keras optimizer, please use `learning_rate` or use the legacy optimizer, e.g.,tf.keras.optimizers.legacy.RMSprop.

history4 = model4.fit_generator(
    train_generator,
    steps_per_epoch=train_generator.n//train_generator.batch_size,
    epochs=20,
    validation_data=validation_generator,
    validation_steps=validation_generator.n//validation_generator.batch_size
)

model4.save('Dermatology_problem_v1_m.h5')

C:\Users\dggua\AppData\Local\Temp\ipykernel_20580\1713391298.py:1: UserWarning: `Model.fit_generator` is deprecated and will be removed in a future version. Please use `Model.fit`, which supports generators.
  history4 = model4.fit_generator(

Epoch 1/20
21/21 [==============================] - 229s 11s/step - loss: 3.7929 - accuracy: 0.2274 - precision: 0.2081 - recall: 0.0358 - f1_m: 0.0368 - f1_weighted: 0.8699 - val_loss: 2.1746 - val_accuracy: 0.2422 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.8589
Epoch 2/20
21/21 [==============================] - 193s 9s/step - loss: 2.1946 - accuracy: 0.2508 - precision: 0.4091 - recall: 0.0035 - f1_m: 0.0059 - f1_weighted: 0.8556 - val_loss: 2.1445 - val_accuracy: 0.2083 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.8585
Epoch 3/20
21/21 [==============================] - 193s 9s/step - loss: 2.1625 - accuracy: 0.2481 - precision: 0.1250 - recall: 3.8880e-04 - f1_m: 7.0028e-04 - f1_weighted: 0.8553 - val_loss: 2.1522 - val_accuracy: 0.2474 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.8613
Epoch 4/20
21/21 [==============================] - 190s 9s/step - loss: 2.1909 - accuracy: 0.2216 - precision: 0.2479 - recall: 0.0117 - f1_m: 0.0125 - f1_weighted: 0.8580 - val_loss: 2.1202 - val_accuracy: 0.2630 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.8486
Epoch 5/20
21/21 [==============================] - 189s 9s/step - loss: 2.1546 - accuracy: 0.2597 - precision: 0.4000 - recall: 0.0016 - f1_m: 0.0028 - f1_weighted: 0.8558 - val_loss: 2.1310 - val_accuracy: 0.2500 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.8453
Epoch 6/20
21/21 [==============================] - 197s 9s/step - loss: 2.1397 - accuracy: 0.2507 - precision: 0.6667 - recall: 7.4405e-04 - f1_m: 0.0015 - f1_weighted: 0.8512 - val_loss: 2.1384 - val_accuracy: 0.2292 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.8433
Epoch 7/20
21/21 [==============================] - 189s 9s/step - loss: 2.1345 - accuracy: 0.2714 - precision: 0.3514 - recall: 0.0051 - f1_m: 0.0081 - f1_weighted: 0.8508 - val_loss: 2.2374 - val_accuracy: 0.2552 - val_precision: 0.3750 - val_recall: 0.0469 - val_f1_m: 0.0827 - val_f1_weighted: 0.8439
Epoch 8/20
21/21 [==============================] - 193s 9s/step - loss: 2.1184 - accuracy: 0.2562 - precision: 0.4348 - recall: 0.0039 - f1_m: 0.0070 - f1_weighted: 0.8464 - val_loss: 2.0953 - val_accuracy: 0.2760 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.8482
Epoch 9/20
21/21 [==============================] - 189s 9s/step - loss: 2.0796 - accuracy: 0.2788 - precision: 0.4058 - recall: 0.0109 - f1_m: 0.0209 - f1_weighted: 0.8404 - val_loss: 2.1454 - val_accuracy: 0.2500 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.8437
Epoch 10/20
21/21 [==============================] - 189s 9s/step - loss: 2.0736 - accuracy: 0.2807 - precision: 0.4286 - recall: 0.0035 - f1_m: 0.0065 - f1_weighted: 0.8401 - val_loss: 2.1259 - val_accuracy: 0.2708 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.8567
Epoch 11/20
21/21 [==============================] - 189s 9s/step - loss: 2.0364 - accuracy: 0.2885 - precision: 0.4583 - recall: 0.0086 - f1_m: 0.0146 - f1_weighted: 0.8300 - val_loss: 2.0777 - val_accuracy: 0.2969 - val_precision: 0.5455 - val_recall: 0.0156 - val_f1_m: 0.0300 - val_f1_weighted: 0.8296
Epoch 12/20
21/21 [==============================] - 191s 9s/step - loss: 2.0524 - accuracy: 0.2846 - precision: 0.4500 - recall: 0.0140 - f1_m: 0.0253 - f1_weighted: 0.8271 - val_loss: 2.0783 - val_accuracy: 0.2708 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.8405
Epoch 13/20
21/21 [==============================] - 187s 9s/step - loss: 2.0020 - accuracy: 0.2951 - precision: 0.5714 - recall: 0.0156 - f1_m: 0.0277 - f1_weighted: 0.8220 - val_loss: 2.0173 - val_accuracy: 0.2682 - val_precision: 0.3750 - val_recall: 0.0078 - val_f1_m: 0.0152 - val_f1_weighted: 0.8241
Epoch 14/20
21/21 [==============================] - 187s 9s/step - loss: 1.9808 - accuracy: 0.3075 - precision: 0.5051 - recall: 0.0194 - f1_m: 0.0402 - f1_weighted: 0.8155 - val_loss: 1.9918 - val_accuracy: 0.2969 - val_precision: 0.7333 - val_recall: 0.0286 - val_f1_m: 0.0547 - val_f1_weighted: 0.8104
Epoch 15/20
21/21 [==============================] - 195s 9s/step - loss: 1.9799 - accuracy: 0.3058 - precision: 0.4936 - recall: 0.0286 - f1_m: 0.0522 - f1_weighted: 0.8137 - val_loss: 1.9550 - val_accuracy: 0.2969 - val_precision: 0.7143 - val_recall: 0.0130 - val_f1_m: 0.0255 - val_f1_weighted: 0.8158
Epoch 16/20
21/21 [==============================] - 188s 9s/step - loss: 1.9697 - accuracy: 0.3103 - precision: 0.5247 - recall: 0.0330 - f1_m: 0.0630 - f1_weighted: 0.8100 - val_loss: 2.0683 - val_accuracy: 0.2734 - val_precision: 0.5333 - val_recall: 0.0208 - val_f1_m: 0.0400 - val_f1_weighted: 0.8325
Epoch 17/20
21/21 [==============================] - 188s 9s/step - loss: 1.9745 - accuracy: 0.3184 - precision: 0.4505 - recall: 0.0389 - f1_m: 0.0647 - f1_weighted: 0.8048 - val_loss: 1.9751 - val_accuracy: 0.2708 - val_precision: 0.5238 - val_recall: 0.0286 - val_f1_m: 0.0544 - val_f1_weighted: 0.8141
Epoch 18/20
21/21 [==============================] - 191s 9s/step - loss: 1.9497 - accuracy: 0.3157 - precision: 0.5176 - recall: 0.0342 - f1_m: 0.0666 - f1_weighted: 0.8053 - val_loss: 1.9916 - val_accuracy: 0.3073 - val_precision: 0.6667 - val_recall: 0.0156 - val_f1_m: 0.0302 - val_f1_weighted: 0.8179
Epoch 19/20
21/21 [==============================] - 188s 9s/step - loss: 1.9443 - accuracy: 0.3122 - precision: 0.5142 - recall: 0.0494 - f1_m: 0.0879 - f1_weighted: 0.7959 - val_loss: 2.0233 - val_accuracy: 0.2969 - val_precision: 0.4667 - val_recall: 0.0182 - val_f1_m: 0.0349 - val_f1_weighted: 0.8206
Epoch 20/20
21/21 [==============================] - 189s 9s/step - loss: 1.9211 - accuracy: 0.3250 - precision: 0.5367 - recall: 0.0540 - f1_m: 0.0914 - f1_weighted: 0.7928 - val_loss: 2.0048 - val_accuracy: 0.2734 - val_precision: 0.5714 - val_recall: 0.0312 - val_f1_m: 0.0585 - val_f1_weighted: 0.8147

Run the whole project to review the answers

#This is the directory where the images are stored 
dw_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/imgPrueba'

#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_3'

test_dir = os.path.join(original_dataset_dir, 'test')

test_generator = test_datagen.flow_from_directory(
    test_dir,
    target_size=(200, 200),
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical',
    
)

Found 3401 images belonging to 3 classes.

First Prediction

predictions = model.predict_generator(test_generator,  verbose = 1)

C:\Users\dggua\AppData\Local\Temp\ipykernel_20580\3388676779.py:1: UserWarning: `Model.predict_generator` is deprecated and will be removed in a future version. Please use `Model.predict`, which supports generators.
  predictions = model.predict_generator(test_generator,  verbose = 1)

27/27 [==============================] - 144s 5s/step

len(predictions)

3401

Seperate the predictions into the three classes through getting the max

a1 = []
a2 = []
a3 = []
atotal = []
for i in predictions:
    
    c=0
    for j in i:
        if(j==max(i)):
            if(c==0):
                a1.append(j)
                atotal.append(0)
            elif(c==1):
                a2.append(j)
                atotal.append(1)
            else:
                a3.append(j)
                atotal.append(2)
        c+=1

Counting how many got right and wrong and saving it in at if is right then either 0, 1, 2 been the classification of the three

If wrong is 4

points = 0
points_w = 0
class_indices = test_generator.classes

at = []
a = len(atotal)
for i in range(0, a):
    if(atotal[i]==class_indices[i]):
        points+=1
        at.append(atotal[i])
    else:
        points_w+=1
        at.append(4)
        
print(points, points_w)
print(points/(points+points_w))
print(Counter(at))

2394 1007
0.7039106145251397
Counter({2: 2374, 4: 1007, 1: 20})

The same as last two steps but this is done based on the probability given in the prediction

points = 0
points_w = 0
c = 0
at = []
y_pred = []
for i in predictions: 
    random_num = round(random.uniform(0, 1), 8)
    classi = 0
    if(random_num <= i[0]):
        classi = 0
    elif((random_num > i[0]) and (random_num<=(i[1]+i[0]))):
        classi = 1
    else:
        classi = 2
    if(classi==class_indices[c]):
        points+=1
        at.append(classi)
    else:
        points_w+=1
        at.append(4)
    y_pred.append(classi)
    c+=1



#bb
f1 = f1_score(class_indices, y_pred, average='macro')
print(points, points_w)
print('accuracy: ',points/(points+points_w))
print('f1:', f1)
print(Counter(at))
print(Counter(class_indices))

2057 1344
accuracy:  0.6048221111437813
f1: 0.33796249803822836
Counter({2: 1951, 4: 1344, 0: 57, 1: 49})
Counter({2: 2472, 0: 467, 1: 462})

Saving each of the batch images on a test array, test_b for belign, test_m for Malignant, test_n for non-neoplastic

test_b = []
test_m = []
test_n = []
test_error = []
count = 0
print(Counter(at))
rangee = test_generator.samples
print(rangee/128)
for i in range(0,27):
    batch_x, batch_y = test_generator[i]
    for j in range(0, len(batch_x)):
        if(at[count]==0):
            test_b.append(batch_x[j])
        elif(at[count]==1):
            test_m.append(batch_x[j])
        elif(at[count]==2):
            
            test_n.append(batch_x[j])
        else:
            test_error.append(batch_x[j])
        count+=1

Counter({2: 1951, 4: 1344, 0: 57, 1: 49})
26.5703125

print(count)
print(len(test_b),len(test_m),len(test_n))

3401
57 49 1951

Optain the file names of each of the results.

file_names = test_generator.filenames
len(at)

3401

dw_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/imgPrueba'

#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img'

test_dir = os.path.join(original_dataset_dir, 'test')

test_generator = test_datagen.flow_from_directory(
    test_dir,
    target_size=(200, 200),
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical',
    
)

Found 3401 images belonging to 114 classes.

From the original data set find the name of the files and check which is the sub class it belongs to in this case which label

From there we save it on an array to save their corresponding label

test_label_b = []
test_label_m = []
test_label_n = []
test_label_error=[]
test_classes = test_generator.classes
file_new_names = test_generator.filenames
for i in range(0, len(file_new_names)):
    word = file_names[i].split("\\")[1]
    completeword = [s for s in file_new_names if word in s]
    if(at[i]==0):
        test_label_b.append(completeword[0].split("\\")[0])
    elif(at[i]==1):
        test_label_m.append(completeword[0].split("\\")[0])
    elif(at[i]==2):
        test_label_n.append(completeword[0].split("\\")[0])
    else:
        test_label_error.append(completeword[0].split("\\")[0])

print(len(test_label_b), len(test_label_m), len(test_label_n))

57 49 1951

Now we optain the information from the folder of image belign

#### First Model. 
#This is the directory where the images are stored 
dw_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/imgPrueba'

#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_b'
#Directories for the training, validation and test splits

# os.mkdir(validation_dit)
test_dir = os.path.join(original_dataset_dir, 'test')
# os.mkdir(test_dir)

train_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True
                                  
                                   #, fill_mode='nearest'
                                   )

test_generator = train_datagen.flow_from_directory(
    test_dir,
    target_size=(200, 200), # This might be resize () Increase the size. (485-364), yeah change it to square?
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical'
)

Found 467 images belonging to 24 classes.

Here we convert the label to binary like [0, 0, 0, 1]

class_indices_b = test_generator.class_indices
test_label_b_bin = []

for i in test_label_b:
    ii = i
    ind = class_indices_b[ii]
    array = np.zeros(24)
    array[ind] = 1
    test_label_b_bin.append(array)

We create our data imagery with the images and labels

test_b = np.array(test_b)
print(len(test_b))

test_generator_b = test_datagen.flow(
    x=test_b,
    y=test_label_b_bin,
    batch_size=128,
)

57

Prediction

predictions22 = model2.predict_generator(test_generator_b,  verbose = 1)

C:\Users\dggua\AppData\Local\Temp\ipykernel_20580\2249938597.py:1: UserWarning: `Model.predict_generator` is deprecated and will be removed in a future version. Please use `Model.predict`, which supports generators.
  predictions22 = model2.predict_generator(test_generator_b,  verbose = 1)

1/1 [==============================] - 2s 2s/step

Assign the labels

b_answer = []
print(predictions22[0])
y_pred = []

for i in predictions22:
    c=0
    random_num = round(random.uniform(0, 1), 8)
    random.shuffle(i)
    c = 0
    m = 0
    for j in i:
        c+= j
        if(random_num<=c):
            b_answer.append(m-1)
            break
        m+=1
print(Counter(b_answer))

print(len(b_answer))

[1.3722775e-05 5.4736453e-04 1.0823730e-03 6.9612749e-02 5.9225131e-03
 4.1214842e-03 2.9216907e-03 5.2480817e-01 2.1112757e-03 5.7951105e-04
 1.1633346e-01 8.0551198e-03 3.8829322e-03 9.8589636e-02 2.4917714e-02
 3.4294818e-02 1.4522140e-06 5.9898250e-04 1.4103074e-03 1.5471301e-04
 9.1186929e-03 5.5088061e-03 8.4991328e-02 4.2131628e-04]
Counter({2: 5, 4: 5, 21: 4, 16: 4, 6: 4, 15: 4, 14: 3, 3: 3, 11: 3, 10: 3, 8: 3, 18: 2, 13: 2, 7: 2, 17: 2, 0: 2, 9: 1, 22: 1, 19: 1, -1: 1, 5: 1, 20: 1})
57

Check how many got right and wrong

points = 0
points_w = 0
a = len(b_answer)
print(a)
y_true = []
print(len(test_label_b_bin))
for i in test_label_b_bin:
    for j in range(0,len(i)):
        if i[j] == 1:
            y_true.append(j)
print(len(y_true))    
for i in range(0, a):
    if(y_true[i]==b_answer[i]):
        points+=1
    else:
        points_w+=1

f1 = f1_score(y_true, b_answer, average='macro')
print(points, points_w)
print('accuracy: ',points/(points+points_w))   
print('f1_m', f1)

57
57
57
0 57
accuracy:  0.0
f1_m 0.0

Same Steps to the next model for non-neoplastic

###Second Model###########
#### First Model. 
#This is the directory where the images are stored 
dw_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/imgPrueba'

#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_n'
#Directories for the training, validation and test splits

# os.mkdir(validation_dit)
test_dir = os.path.join(original_dataset_dir, 'test')
# os.mkdir(test_dir)

train_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True
                                  
                                   #, fill_mode='nearest'
                                   )

test_generator = train_datagen.flow_from_directory(
    test_dir,
    target_size=(200, 200), # This might be resize () Increase the size. (485-364), yeah change it to square?
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical'
)

Found 2472 images belonging to 79 classes.

class_indices_n = test_generator.class_indices
test_label_n_bin = []

for i in test_label_n:
    ind = class_indices_n[i]
    array = np.zeros(79)
    array[ind] = 1
    test_label_n_bin.append(array)

test_n = np.array(test_n)
test_generator_n = test_datagen.flow(
    x=test_n,
    y=test_label_n_bin,
    batch_size=128,
)

predictions3 = model3.predict_generator(test_generator_n,  verbose = 1)

C:\Users\dggua\AppData\Local\Temp\ipykernel_20580\595569640.py:1: UserWarning: `Model.predict_generator` is deprecated and will be removed in a future version. Please use `Model.predict`, which supports generators.
  predictions3 = model3.predict_generator(test_generator_n,  verbose = 1)

16/16 [==============================] - 47s 3s/step

n_answer = []

y_pred = []

for i in predictions3:
    c=0
    random_num = round(random.uniform(0, 1), 8)
    random.shuffle(i)
    c = 0
    m = 0
    for j in i:
        c+= j
        if(random_num<=c):
            n_answer.append(m-1)
            break
        m+=1
print(Counter(n_answer))

print(len(n_answer))

Counter({49: 38, 5: 35, 32: 34, 19: 34, 50: 33, 41: 33, 6: 32, 30: 31, 29: 31, 9: 30, 38: 30, 73: 29, 60: 29, 51: 29, 42: 29, 20: 29, -1: 28, 11: 28, 0: 28, 28: 28, 22: 28, 65: 27, 56: 27, 43: 27, 58: 27, 55: 27, 72: 27, 31: 26, 76: 26, 37: 26, 54: 26, 53: 26, 39: 25, 68: 25, 45: 25, 57: 24, 4: 24, 75: 24, 15: 24, 33: 24, 34: 24, 71: 24, 48: 24, 59: 24, 77: 24, 12: 23, 2: 23, 24: 23, 66: 23, 64: 23, 14: 23, 40: 23, 7: 22, 69: 22, 10: 22, 36: 22, 67: 22, 44: 22, 3: 22, 46: 22, 25: 22, 8: 22, 1: 21, 18: 21, 13: 21, 21: 20, 74: 20, 70: 19, 26: 19, 62: 19, 17: 19, 47: 18, 61: 18, 35: 18, 52: 18, 16: 17, 63: 17, 27: 16, 23: 16})
1951

Result how many right and wrongs

points = 0
points_w = 0
a = len(n_answer)

y_true = []

for i in test_label_n_bin:
    for j in range(0,len(i)):
        if i[j] == 1:
            y_true.append(j)
print(len(y_true))    
for i in range(0, a):
    if(y_true[i]==n_answer[i]):
        points+=1
    else:
        points_w+=1

f1 = f1_score(y_true, n_answer, average='macro')
print(points, points_w)
print('accuracy: ',points/(points+points_w))   
print('f1_m', f1)

1951
20 1931
accuracy:  0.010251153254741158
f1_m 0.00935697037718827

For Last model Malignant

###Third Model###########
#### First Model. 
#This is the directory where the images are stored 
dw_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/imgPrueba'

#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_m'
#Directories for the training, validation and test splits

# os.mkdir(validation_dit)
test_dir = os.path.join(original_dataset_dir, 'test')
# os.mkdir(test_dir)

train_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True
                                  
                                   #, fill_mode='nearest'
                                   )

test_generator = train_datagen.flow_from_directory(
    test_dir,
    target_size=(200, 200), # This might be resize () Increase the size. (485-364), yeah change it to square?
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical'
)

Found 462 images belonging to 11 classes.

class_indices_m = test_generator.class_indices
test_label_m_bin = []

for i in test_label_m:
    ind = class_indices_m[i]
    array = np.zeros(11)
    array[ind] = 1
    test_label_m_bin.append(array)

test_m = np.array(test_m)
test_generator_m = test_datagen.flow(
    x=test_m,
    y=test_label_m_bin,
    batch_size=128,
)

predictions4 = model4.predict_generator(test_generator_m,  verbose = 1)

C:\Users\dggua\AppData\Local\Temp\ipykernel_20580\3950755775.py:1: UserWarning: `Model.predict_generator` is deprecated and will be removed in a future version. Please use `Model.predict`, which supports generators.
  predictions4 = model4.predict_generator(test_generator_m,  verbose = 1)

1/1 [==============================] - 1s 1s/step

m_answer = []

y_pred = []

for i in predictions4:
    c=0
    random_num = round(random.uniform(0, 1), 8)
    random.shuffle(i)
    c = 0
    m = 0
    for j in i:
        c+= j
        if(random_num<=c):
            m_answer.append(m)
            break
        m+=1
print(Counter(m_answer))

print(len(n_answer))

Counter({3: 8, 8: 6, 10: 6, 5: 6, 9: 5, 1: 5, 6: 5, 4: 3, 2: 2, 0: 2, 7: 1})
1951

Result

points = 0
points_w = 0
a = len(m_answer)

y_true = []

for i in test_label_m_bin:
    for j in range(0,len(i)):
        if i[j] == 1:
            y_true.append(j)
print(len(y_true))    
for i in range(0, a):
    if(y_true[i]==m_answer[i]):
        points+=1
    else:
        points_w+=1
print(len(m_answer))
f1 = f1_score(y_true, m_answer, average='macro')
print(points, points_w)
print('accuracy: ',points/(points+points_w))   
print('f1_m', f1)

49
49
1 48
accuracy:  0.02040816326530612
f1_m 0.0202020202020202